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          <h1 class="post-title" itemprop="name headline">Amber 14 单核版+并行版安装
              
            
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        <font size="4" face="黑体">更新日志</font> 

<blockquote>
<p>2017-02-19: 创建</p>
</blockquote>
<hr>
<h2 id="需要的东西："><a href="#需要的东西：" class="headerlink" title="需要的东西："></a><strong>需要的东西：</strong></h2><ul>
<li>一些底层的函数库</li>
<li>Amber 14 </li>
<li>AmberTools 14</li>
<li>openMPI （安装并行版所需）</li>
<li>linux环境（例如：CentOS 6.8）</li>
</ul>
<h2 id="安装步骤："><a href="#安装步骤：" class="headerlink" title="安装步骤："></a><strong>安装步骤：</strong></h2><h3 id="1-安装底层函数库"><a href="#1-安装底层函数库" class="headerlink" title="1. 安装底层函数库"></a>1. 安装底层函数库</h3><figure class="highlight plain"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br></pre></td><td class="code"><pre><span class="line">yum install libXt-devel libXext-devel libX11-devel \</span><br><span class="line">            libICE-devel libSM-devel fftw.x86_64</span><br></pre></td></tr></table></figure>
<h3 id="2-安装Amber单核版"><a href="#2-安装Amber单核版" class="headerlink" title="2. 安装Amber单核版"></a>2. 安装Amber单核版</h3><ul>
<li>解压Amber14和AmberTools14安装包<code>tar zxcf 文件名</code></li>
<li><p>添加以下内容到 <code>.bashrc</code>文件</p>
<figure class="highlight plain"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br></pre></td><td class="code"><pre><span class="line"># Amber14 setup</span><br><span class="line">export AMBERHOME=&quot;Amber所在的目录&quot;</span><br></pre></td></tr></table></figure>
</li>
<li><p>编译，终端下执行</p>
<figure class="highlight sh"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br></pre></td><td class="code"><pre><span class="line"><span class="built_in">cd</span> <span class="variable">$AMBERHOME</span></span><br><span class="line">./configure gnu</span><br><span class="line">make install</span><br></pre></td></tr></table></figure>
</li>
</ul>
<h3 id="3-安装-openMPI"><a href="#3-安装-openMPI" class="headerlink" title="3. 安装 openMPI"></a>3. 安装 openMPI</h3><ul>
<li>解压openMPI安装包 <code>tar zxcf 文件名</code></li>
<li><p>编译，终端输入</p>
<figure class="highlight sh"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br></pre></td><td class="code"><pre><span class="line"><span class="built_in">cd</span> /home/当前用户名</span><br><span class="line">mkdir openmpi_after_compile</span><br><span class="line"><span class="built_in">cd</span> <span class="string">"openMPI所在的目录"</span></span><br><span class="line">./configure --prefix=/home/当前用户名/openmpi_after_compile</span><br><span class="line">make install</span><br></pre></td></tr></table></figure>
</li>
<li><p>添加以下内容到 <code>.bashrc</code>文件</p>
<figure class="highlight sh"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br></pre></td><td class="code"><pre><span class="line"><span class="comment"># openMPI setup</span></span><br><span class="line"><span class="built_in">export</span> MPI_HOME=/home/当前用户名/openmpi_after_compile</span><br><span class="line"><span class="built_in">export</span> PATH=<span class="variable">$PATH</span>:<span class="variable">$MPI_HOME</span>/bin</span><br><span class="line"><span class="built_in">export</span> LD_LIBRARY_PATH=<span class="variable">$LD_LIBRARY_PATH</span>:<span class="variable">$MPI_HOME</span>/lib</span><br></pre></td></tr></table></figure>
</li>
</ul>
<h3 id="4-安装Amber并行版"><a href="#4-安装Amber并行版" class="headerlink" title="4. 安装Amber并行版"></a>4. 安装Amber并行版</h3><ul>
<li><p>编译，终端输入</p>
<figure class="highlight sh"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br></pre></td><td class="code"><pre><span class="line"><span class="built_in">cd</span> <span class="variable">$AMBERHOME</span></span><br><span class="line">make clean</span><br><span class="line">./configure -mpi gnu</span><br><span class="line">make install</span><br></pre></td></tr></table></figure>
</li>
<li><p>添加以下内容到 <code>.bashrc</code>文件</p>
<figure class="highlight sh"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br></pre></td><td class="code"><pre><span class="line"><span class="comment"># Amber14 setup</span></span><br><span class="line"><span class="built_in">export</span> AMBERHOME=<span class="string">"Amber所在的目录"</span></span><br><span class="line"><span class="built_in">export</span> LD_LIBRARY_PATH=<span class="variable">$LD_LIBRARY_PATH</span>:<span class="variable">$AMBERHOME</span>/lib</span><br><span class="line"><span class="built_in">export</span> PATH=<span class="variable">$PATH</span>:<span class="variable">$AMBERHOME</span>/bin</span><br><span class="line"><span class="built_in">export</span> DO_PARARRLE=<span class="string">"mpirun -np 8"</span></span><br></pre></td></tr></table></figure>
</li>
</ul>
<h3 id="5-对Amber运行情况进行测试（可选）"><a href="#5-对Amber运行情况进行测试（可选）" class="headerlink" title="5. 对Amber运行情况进行测试（可选）"></a>5. 对Amber运行情况进行测试（可选）</h3><ul>
<li><p>终端输入</p>
<figure class="highlight plain"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br></pre></td><td class="code"><pre><span class="line">cd $AMBERHOME/test</span><br><span class="line">make</span><br><span class="line"># 测试Amber单核版</span><br><span class="line">./test_amber_serial.sh &gt;&amp;test_serial.log&amp;</span><br><span class="line"># 测试Amber并行版</span><br><span class="line">./test_amber_clean.sh</span><br><span class="line">./test_amber_parallel.sh &gt;&amp;test_parallel.log&amp;</span><br><span class="line"></span><br><span class="line">cd $AMBERHOME/AmberTools/test</span><br><span class="line"># 测试AmberTools单核版</span><br><span class="line">./test_at_serial.sh &gt;&amp;test_serial.log&amp;</span><br><span class="line"># 测试AmberTools并行版</span><br><span class="line">./test_at_parallel.sh &gt;&amp;test_parallel.log&amp;</span><br></pre></td></tr></table></figure>
</li>
<li><p>查看生成的4个<code>.log</code>文件，获取Amber运行情况</p>
</li>
</ul>

      
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